Mission managers who were packed into the New Horizons "mission control" room anxiously waiting to hear from the spacecraft broke into applause.
The probe had spent more than 12 hours out of contact while it collected data from Pluto and its five moons.
The communications outage was planned, but it still had scientists on edge. The flyby was the most dangerous part of the mission; there was a chance that stray dust in the Pluto system could collide with the spacecraft.
NASA administrator Charles Bolden joined mission manager Alice Bowman to congratulate the team in the mission operations center. Bowman said the probe is healthy and "outbound" from Pluto.
NASA opened its flyby "phone home" briefing with a congratulatory message from Stephen Hawking.
The unmanned piano-size spacecraft went over Pluto at 7:49 a.m. ET, traveling at nearly 31,000 mph about 7,750 miles above Pluto's surface, NASA said.
